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PDBsum entry 1ykw

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protein Protein-protein interface(s) links
Unknown function PDB id
1ykw
Jmol
Contents
Protein chains
414 a.a. *
Waters ×317
* Residue conservation analysis
PDB id:
1ykw
Name: Unknown function
Title: Crystal structure of a novel rubisco-like protein from the g sulfur bacterium chlorobium tepidum
Structure: Rubisco-like protein. Chain: a, b. Engineered: yes. Mutation: yes
Source: Chlorobaculum tepidum. Organism_taxid: 1097. Gene: ct1772. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.203     R-free:   0.245
Authors: H.Li,M.R.Sawaya,F.R.Tabita,D.Eisenberg
Key ref:
H.Li et al. (2005). Crystal structure of a RuBisCO-like protein from the green sulfur bacterium Chlorobium tepidum. Structure, 13, 779-789. PubMed id: 15893668 DOI: 10.1016/j.str.2005.02.017
Date:
18-Jan-05     Release date:   17-May-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q8KBL4  (RBLL_CHLTE) -  Ribulose bisphosphate carboxylase-like protein
Seq:
Struc:
435 a.a.
414 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbon fixation   1 term 
  Biochemical function     metal ion binding     3 terms  

 

 
DOI no: 10.1016/j.str.2005.02.017 Structure 13:779-789 (2005)
PubMed id: 15893668  
 
 
Crystal structure of a RuBisCO-like protein from the green sulfur bacterium Chlorobium tepidum.
H.Li, M.R.Sawaya, F.R.Tabita, D.Eisenberg.
 
  ABSTRACT  
 
Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) catalyzes the incorporation of atmospheric CO(2) into ribulose 1,5-bisphosphate (RuBP). RuBisCOs are classified into four forms based on sequence similarity: forms I, II and III are bona fide RuBisCOs; form IV, also called the RuBisCO-like protein (RLP), lacks several of the substrate binding and catalytic residues and does not catalyze RuBP-dependent CO(2) fixation in vitro. To contribute to understanding the function of RLPs, we determined the crystal structure of the RLP from Chlorobium tepidum. The overall structure of the RLP is similar to the structures of the three other forms of RuBisCO; however, the active site is distinct from those of bona fide RuBisCOs and suggests that the RLP is possibly capable of catalyzing enolization but not carboxylation. Bioinformatic analysis of the protein functional linkages suggests that this RLP coevolved with enzymes of the bacteriochlorophyll biosynthesis pathway and may be involved in processes related to photosynthesis.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Loop 6 and Loop CD in the RuBisCO Structures
C. tepidum RLP is colored in dark pink, activated spinach RuBisCO (8RUC) is colored in blue, unactivated tobacco RuBisCO (1EJ7) is colored in yellow, and unactivated R. rubrum RuBisCO (5RUB) is colored in green. Loop 6 is in an open conformation in the tobacco RuBisCO as shown by the yellow loop in 1EJ7 structure. It is disordered in 5RUB structure (not modeled) as shown by the broken green structure. Loop 6 is in a closed conformation in the spinach RuBisCO structure, as shown by the blue loop in the 8RUC structure. It folds over the active site and shields the substrate from the solvent. In the RLP structure, loop 6 has a similar closed conformation as in 8RUC. Loop CD in the RLP structure is an extended insertion between b strands C and D. This loop folds over the side of the b sheet in the N-terminal domain and closes the active site further outside of loop 6 from an opposite direction. In the other RuBisCO structures, there is only a short loop between b strands C and D. The tip of the loop CD in the RLP is partially aligned with the C-terminal tail b strand in the activated form I RuBisCO structure (8RUC), which becomes ordered and extends toward the active site packing against loop 6 upon RuBP or transition-state analog binding. The axis of the a/b barrel is indicated with an arrow. Only parts of the structures are shown for the purpose of clarity.
 
  The above figure is reprinted by permission from Cell Press: Structure (2005, 13, 779-789) copyright 2005.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20038587 J.Singh, and F.R.Tabita (2010).
Roles of RubisCO and the RubisCO-like protein in 5-methylthioadenosine metabolism in the Nonsulfur purple bacterium Rhodospirillum rubrum.
  J Bacteriol, 192, 1324-1331.  
  19194007 H.Tamura, H.Ashida, S.Koga, Y.Saito, T.Yadani, Y.Kai, T.Inoue, A.Yokota, and H.Matsumura (2009).
Crystallization and preliminary X-ray analysis of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase from Bacillus subtilis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 147-150.  
19690372 H.Tamura, Y.Saito, H.Ashida, Y.Kai, T.Inoue, A.Yokota, and H.Matsumura (2009).
Structure of the apo decarbamylated form of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase from Bacillus subtilis.
  Acta Crystallogr D Biol Crystallogr, 65, 942-951.
PDB code: 2zvi
19557347 J.H.Lee, D.O.Park, S.W.Park, E.H.Hwang, J.I.Oh, and Y.M.Kim (2009).
Expression and regulation of ribulose 1,5-bisphosphate carboxylase/oxygenase genes in Mycobacterium sp. strain JC1 DSM 3803.
  J Microbiol, 47, 297-307.  
18487131 F.R.Tabita, T.E.Hanson, S.Satagopan, B.H.Witte, and N.E.Kreel (2008).
Phylogenetic and evolutionary relationships of RubisCO and the RubisCO-like proteins and the functional lessons provided by diverse molecular forms.
  Philos Trans R Soc Lond B Biol Sci, 363, 2629-2640.  
18344346 G.J.Dick, S.Podell, H.A.Johnson, Y.Rivera-Espinoza, R.Bernier-Latmani, J.K.McCarthy, J.W.Torpey, B.G.Clement, T.Gaasterland, and B.M.Tebo (2008).
Genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85-9A1.
  Appl Environ Microbiol, 74, 2646-2658.  
18826254 H.J.Imker, J.Singh, B.P.Warlick, F.R.Tabita, and J.A.Gerlt (2008).
Mechanistic diversity in the RuBisCO superfamily: a novel isomerization reaction catalyzed by the RuBisCO-like protein from Rhodospirillum rubrum.
  Biochemistry, 47, 11171-11173.  
18063718 F.R.Tabita, T.E.Hanson, H.Li, S.Satagopan, J.Singh, and S.Chan (2007).
Function, structure, and evolution of the RubisCO-like proteins and their RubisCO homologs.
  Microbiol Mol Biol Rev, 71, 576-599.
PDB code: 2qyg
17024516 H.E.Elsaied, H.Kimura, and T.Naganuma (2007).
Composition of archaeal, bacterial, and eukaryal RuBisCO genotypes in three Western Pacific arc hydrothermal vent systems.
  Extremophiles, 11, 191-202.  
17355171 S.Yooseph, G.Sutton, D.B.Rusch, A.L.Halpern, S.J.Williamson, K.Remington, J.A.Eisen, K.B.Heidelberg, G.Manning, W.Li, L.Jaroszewski, P.Cieplak, C.S.Miller, H.Li, S.T.Mashiyama, M.P.Joachimiak, C.van Belle, J.M.Chandonia, D.A.Soergel, Y.Zhai, K.Natarajan, S.Lee, B.J.Raphael, V.Bafna, R.Friedman, S.E.Brenner, A.Godzik, D.Eisenberg, J.E.Dixon, S.S.Taylor, R.L.Strausberg, M.Frazier, and J.C.Venter (2007).
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families.
  PLoS Biol, 5, e16.  
17098896 W.D.Swingley, S.Sadekar, S.D.Mastrian, H.J.Matthies, J.Hao, H.Ramos, C.R.Acharya, A.L.Conrad, H.L.Taylor, L.C.Dejesa, M.K.Shah, M.E.O'huallachain, M.T.Lince, R.E.Blankenship, J.T.Beatty, and J.W.Touchman (2007).
The complete genome sequence of Roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism.
  J Bacteriol, 189, 683-690.  
16737967 A.Carré-Mlouka, A.Méjean, P.Quillardet, H.Ashida, Y.Saito, A.Yokota, I.Callebaut, A.Sekowska, E.Dittmann, C.Bouchier, and N.T.de Marsac (2006).
A new rubisco-like protein coexists with a photosynthetic rubisco in the planktonic cyanobacteria Microcystis.
  J Biol Chem, 281, 24462-24471.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.